Genus classification compares sequence representations on separate simulated amplicon and shotgun datasets.
Amplicon and shotgun collections derived from RDP version 11 update 5 (30 September 2016), with balanced taxonomic subsets and a separate unbalanced Qiita collection. The taxonomic label level and sequence-generation method must remain attached to each evaluation.
Classification accuracy at multiple ranks; the genus task must be distinguished from easier higher-rank outcomes.
Sequence-derived PC-mer or alternative feature encodings.
Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.
limited source coverage · Automated source review, 2026-09-16. All specifications and missing details
Results are available, but no reviewed comparison panel is linked in this release.
1 evaluation · 1 result. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Pipeline: PC-mer + LR | Task: metagenomic genus classification Dataset: AMP | 97% accuracy percent · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcePC-mer + LR: metagenomic genus classification k=8 PC-mer feature extraction with logistic regression on AMP genus-classification dataset Aggregation: Not reported PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Table 3, AMP section, PC-mer + LR k=8 row, Accuracy (%) column |
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
Amplicon and shotgun collections derived from RDP version 11 update 5 (30 September 2016), with balanced taxonomic subsets and a separate unbalanced Qiita collection. The taxonomic label level and sequence-generation method must remain attached to each evaluation. Ten-fold cross-validation is reported for the benchmark experiments. Classification accuracy at multiple ranks; the genus task must be distinguished from easier higher-rank outcomes. Conventional classifiers using PC-mer are compared with CNN/DBN approaches using alternative encodings. The study evaluates supervised classifiers with ten-fold cross-validation across the amplicon and shotgun collections. Sections 2.2 and 3.1–3.5 do not specify genome-, species- or homology-grouped fold assignment; ten-fold evaluation alone does not establish unseen-species generalization.
Each evaluation records what was tested and under which conditions.
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No source-reviewed explanatory claims are recorded here yet.
Targeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change.
Stable record: reported-task-4420dcdfe8338dExplanatory profile: limited source coverage · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Datasets | Amplicon and shotgun collections derived from RDP version 11 update 5 (30 September 2016), with balanced taxonomic subsets and a separate unbalanced Qiita collection. The taxonomic label level and sequence-generation method must remain attached to each evaluation.SourcesPC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Results 3.1 Datasets |
| Splits | Ten-fold cross-validation is reported for the benchmark experiments.SourcesPC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 |
| Metrics | Classification accuracy at multiple ranks; the genus task must be distinguished from easier higher-rank outcomes.SourcesPC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 |
| Baselines | Conventional classifiers using PC-mer are compared with CNN/DBN approaches using alternative encodings.SourcesPC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 |
| Leakage controls | The study evaluates supervised classifiers with ten-fold cross-validation across the amplicon and shotgun collections. Sections 2.2 and 3.1–3.5 do not specify genome-, species- or homology-grouped fold assignment; ten-fold evaluation alone does not establish unseen-species generalization. · Not reported in inspected sourcesSourcesPC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Methods 2.2 Learning unit; Results 3.1 Datasets and 3.5.1 Training and testing procedure |
| Uncertainty | The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim. · Not reported in inspected sourcesSourcesPC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 |
| Entity type | Paper-specific computational evaluation protocol.SourcesPC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 |
| Organisms | Simulated microbial amplicon and shotgun communities.SourcesPC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 |
| Assays | Genus-level taxonomic labels.SourcesPC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 |
| Allowed inputs | Sequence-derived PC-mer or alternative feature encodings.SourcesPC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 |
| Adaptation | Supervised classifiers evaluated through ten-fold cross-validation.SourcesPC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification · Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 |
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Last literature check: 2026-09-17. Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
| Paper or primary resource | Version | Reference |
|---|---|---|
| PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification | version of record | Read source DOI: 10.1371/journal.pone.0307279 |
The catalogue now holds 1 result rows for this benchmark. A note below about pending extraction describes the state on 2026-09-17 and may since have been answered by a later batch. The result rows and their sources are the current record.
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Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
17 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol. Individual claims | PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Diagram steps
| PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Computational evaluation flow Individual claims | PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Datasets Amplicon and shotgun collections derived from RDP version 11 update 5 (30 September 2016), with balanced taxonomic subsets and a separate unbalanced Qiita collection. The taxonomic label level and sequence-generation method must remain attached to each evaluation. Individual claims | PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification Results 3.1 Datasets Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Splits Ten-fold cross-validation is reported for the benchmark experiments. Individual claims | PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Adaptation Supervised classifiers evaluated through ten-fold cross-validation. Individual claims | PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Metrics Classification accuracy at multiple ranks; the genus task must be distinguished from easier higher-rank outcomes. Individual claims | PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Baselines Conventional classifiers using PC-mer are compared with CNN/DBN approaches using alternative encodings. Individual claims | PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Leakage controls The study evaluates supervised classifiers with ten-fold cross-validation across the amplicon and shotgun collections. Sections 2.2 and 3.1–3.5 do not specify genome-, species- or homology-grouped fold assignment; ten-fold evaluation alone does not establish unseen-species generalization. Individual claims | PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification Methods 2.2 Learning unit; Results 3.1 Datasets and 3.5.1 Training and testing procedure Version: version of record | unreported automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Uncertainty The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim. Individual claims | PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification Methods §3.1; Results/Conclusion; cached text lines 23–24, 48, 58 Version: version of record | unreported automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
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Release 2026-09-29-06401fd5b220 · Record review: needs review
Stable ID: reported-task-4420dcdfe8338d